Research workbench
The crystal structure of a putative transcriptional regulator from vibrio parahaemolyticus
Analyse The crystal structure of a putative transcriptional regulator from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OXN
- Type
- protein
- Length
- 853 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative transcriptional regulator, lysr family
- UniProt
- Q87TP2
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative transcriptional regulator, lysr family | protein | 213 | 40% helix, 25% strand | Q87TP2 |
| B | Putative transcriptional regulator, lysr family | protein | 215 | 37% helix, 21% strand | Q87TP2 |
| C | Putative transcriptional regulator, lysr family | protein | 213 | 38% helix, 26% strand | Q87TP2 |
| D | Putative transcriptional regulator, lysr family | protein | 212 | 41% helix, 26% strand | Q87TP2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.73 | 0.83 | 57 | empty |
| 2 | 416 | 0.72 | 0.83 | 64 | SO4 |
| 3 | 50 | 0.59 | 0.92 | 12 | empty |
| 4 | 253 | 0.50 | 0.75 | 36 | empty |
| 5 | 78 | 0.50 | 0.83 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1485 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1444 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 221 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 206 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 85 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3OXN · The crystal structure of a putative transcriptional regulator from Vibrio parahaemolyticus · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q87TP2
- Elsewhere: RCSB PDB 3OXN · PDBe 3OXN · UniProt Q87TP2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.